Common stress transcriptome analysis reveals functional and genomic architecture differences between early and delayed response genes

Chung Wen Lin, Li Yao Huang, Chao-Li Huang, Yong Chuan Wang, Pei Hsuan Lai, Hao-Ven Wang, Wen-Chi Chang, Tzen-Yuh Chiang, Hao-Jen Huang

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/ synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.

Original languageEnglish
Pages (from-to)546-559
Number of pages14
JournalPlant and Cell Physiology
Volume58
Issue number3
DOIs
Publication statusPublished - 2017 Mar 1

Fingerprint

Gene Expression Profiling
transcriptomics
genomics
Genes
genes
ferulic acid
exons
introns
Introns
Exons
rice
gene induction
CpG Islands
chromium
transcriptome
Chromium
mercury
lipid metabolism
Mercury
Transcriptome

All Science Journal Classification (ASJC) codes

  • Physiology
  • Plant Science
  • Cell Biology

Cite this

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abstract = "To identify the similarities among responses to diverse environmental stresses, we analyzed the transcriptome response of rice roots to three rhizotoxic perturbations (chromium, ferulic acid and mercury) and identified common early-transient, early-constant and delayed gene inductions. Common early response genes were mostly associated with signal transduction and hormones, and delayed response genes with lipid metabolism. Network component analysis revealed complicated interactions among common genes, the most highly connected signaling hubs being PP2C68, MPK5, LRR-RLK and NPR1. Gene architecture studies revealed different conserved promoter motifs and a different ratio of CpG island distribution between early and delayed genes. In addition, early-transient genes had more exons and a shorter first exon. IMEter was used to calculate the transcription regulation effects of introns, with greater effects for the first introns of early-transient than delayed genes. The higher Ka/Ks (non-synonymous/ synonymous mutation) ratio of early-constant genes than early-transient, delayed and the genome median demonstrates the rapid evolution of early-constant genes. Our results suggest that finely tuned transcriptional control in response to environmental stress in rice depends on genomic architecture and signal intensity and duration.",
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Common stress transcriptome analysis reveals functional and genomic architecture differences between early and delayed response genes. / Lin, Chung Wen; Huang, Li Yao; Huang, Chao-Li; Wang, Yong Chuan; Lai, Pei Hsuan; Wang, Hao-Ven; Chang, Wen-Chi; Chiang, Tzen-Yuh; Huang, Hao-Jen.

In: Plant and Cell Physiology, Vol. 58, No. 3, 01.03.2017, p. 546-559.

Research output: Contribution to journalArticle

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AU - Wang, Hao-Ven

AU - Chang, Wen-Chi

AU - Chiang, Tzen-Yuh

AU - Huang, Hao-Jen

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